Merge pull request #71 from nichollsh/hn/aqua

AQUA notebook and docs

deps/build.jl

@@ -6,6 +6,10 @@ println("ROOT_DIR = $ROOT_DIR")
 RAD_DIR = abspath(ENV["RAD_DIR"])
 println("RAD_DIR = $RAD_DIR")
 
+# Get socrates version
+SOC_VER = readchomp(joinpath(RAD_DIR,"version"))
+println("SOC_VER = $SOC_VER")
+
 # Generate wrappers
 println("Generate wrappers")
 wrap = joinpath(RAD_DIR, "julia/src/generate_wrappers.jl")

docs/src/setup.md

@@ -18,7 +18,7 @@ Follow the steps below in order to setup the code.
 3. Change directory: `cd AGNI`
 4. Setup SOCRATES by doing either **ONE** of the following...
     - Follow the instructions on the [SOCRATES GitHub](https://github.com/nichollsh/SOCRATES) page
-    - Run `source get_socrates.sh`
+    - Run `source src/get_socrates.sh`
 5. `julia -e 'using Pkg; Pkg.activate("."); Pkg.build()'`
 AGNI is now installed as a package into a Julia environment in the AGNI
 directory. This will also have downloaded some basic input data.
@@ -36,6 +36,11 @@ julia ./test/runtests.jl
 ```
 This will print information on whether tests passed or failed.
 
+## Coupling with FastChem
+This can be enabled using the configuration file parameter `composition.chem_type`. Of
+course, it is first necessary to setup FastChem, which can be done by running
+`source src/get_fastchem.sh` and then setting the `FC_DIR` environment variable.
+
 ## Using the code
 See [Running the model](@ref) for information on using the code.
 See [Troubleshooting](@ref) for troubleshooting advice.

docs/src/troubleshooting.md

@@ -19,20 +19,26 @@ official website.
 ## Cannot find SOCRATES
 Check the installation instructions. Have you set `RAD_DIR`? Try running
 `l_run_cdf` in the terminal; if this fails, then SOCRATES has not compiled
-or you haven't added it to your `PATH`.
+or you haven't added it to your `PATH`. It is necessary to set the `RAD_DIR` variable
+for the environment in which you are running AGNI, so it is best to add it to your shell's
+rc file permanently.
 
 
 ## Spectral file does not exist
 Check the path in the configuration file. Download additional spectral files using the
-`get_data` script in the AGNI root directory. For example, for additional pure-steam
-spectral files you would run
+`get_data` script. For example, for additional pure-steam spectral files you would run
 ```bash
 ./src/get_data.sh steam
 ```
 
+## Cannot find FastChem
+You need to install FastChem. This can be done by running the command:
+```bash
+./src/get_fastchem.sh
+```
+and then adding `FC_DIR` to your shell rc file.
 
 ## Finally...
 If you are still stuck, or feel that there is a problem with the code, then
 you can contact the authors using the information on the main page.
 
-

docs/src/usage.md

@@ -8,7 +8,7 @@ If you require more data, such as additional stellar spectra or opacities, then
 also be easily obtained using the `get_data` script in the AGNI root directory. To see how
 to use this script, run it without arguments like so:
 ```bash
-./get_data.sh
+./src/get_data.sh
 ```
 
 ## Tutorials
@@ -17,8 +17,8 @@ of the repository.
 
 ## General execution
 The environment variable `RAD_DIR` must point to the SOCRATES installation
-directory. This is required for AGNI to find the SOCRATES libraries, and can be
-done by running `source path/to/socrates/set_rad_env` in your terminal.
+directory. This is required for AGNI to find the SOCRATES libraries. The best way to do
+this is to add `RAD_DIR=path/to/socrates/folder/` to your shell rc file (e.g. `~/.bashrc`).
 
 Then to use the model, simply run `./agni.jl [cfg]` where `[cfg]` is the path
 to the required configuration file. If `[cfg]` is not passed, then the default

src/AGNI.jl

@@ -11,7 +11,7 @@ module AGNI
     # Include system libraries
     using LoggingExtras
     using Printf
-    using TOML
+    import TOML:parsefile
 
     # Include local jl files (order matters)
     include("phys.jl")
@@ -132,7 +132,7 @@ module AGNI
     function open_config(cfg_path::String)::Dict
 
         # open file
-        cfg_dict = TOML.parsefile(cfg_path)
+        cfg_dict = parsefile(cfg_path)
 
         # check headers
         headers = ["plots", "planet", "files", "execution", "title"]

src/atmosphere.jl

@@ -10,12 +10,12 @@ module atmosphere
 
     # System libraries
     using Printf
-    using DelimitedFiles
-    using PCHIPInterpolation
     using LinearAlgebra
-    using Statistics
     using Logging
     using LoopVectorization
+    # import Statistics
+    import PCHIPInterpolation:Interpolator
+    import DelimitedFiles:readdlm
 
     # Local files
     include(joinpath(ENV["RAD_DIR"],"julia/src/SOCRATES.jl"))
@@ -323,6 +323,8 @@ module atmosphere
             mkdir(OUT_DIR)
         end
 
+        @info "Setting-up a new atmosphere struct"
+
         # Code versions
         atmos.AGNI_VERSION = "0.10.0"
         atmos.SOCRATES_VERSION = readchomp(joinpath(ENV["RAD_DIR"],"version"))
@@ -467,7 +469,7 @@ module atmosphere
 
         # Dict input case
         if mf_source == 0
-            @info "Composition set by dict"
+            @debug "Composition set by dict"
             for (key, value) in mf_dict  # store as arrays
                 gas_valid = strip(key, [' ','\t','\n'])
 
@@ -492,7 +494,7 @@ module atmosphere
                 @error "Could not read VMR file '$mf_path'"
                 return false
             end
-            @info "Composition set by file"
+            @debug "Composition set by file"
 
             # get header
             mf_head::String =   readline(abspath(mf_path))
@@ -669,13 +671,15 @@ module atmosphere
             atmos.FC_DIR = abspath(ENV["FC_DIR"])
             if !isdir(atmos.FC_DIR)
                 @error "Could not find fastchem folder at '$(atmos.FC_DIR)'"
+                @error "Install FastChem with `\$ ./src/get_fastchem.sh`"
                 return false
             end
 
             # check executable
             atmos.fastchem_flag = isfile(joinpath(atmos.FC_DIR,"fastchem"))
             if !atmos.fastchem_flag
-                @error "Could not find fastchem executable inside '$(atmos.FC_DIR)' "
+                @error "Could not find fastchem executable inside '$(atmos.FC_DIR)'"
+                @error "Install FastChem with `\$ ./src/get_fastchem.sh`"
                 return false
             else
                 @info "Found FastChem executable"
@@ -926,6 +930,7 @@ module atmosphere
         # Validate files
         if !isfile(atmos.spectral_file)
             @error "Spectral file '$(atmos.spectral_file)' does not exist"
+            @error "Try running `\$ ./src/get_data.sh`"
             return false
         end
 
@@ -939,6 +944,7 @@ module atmosphere
 
             if !isfile(stellar_spectrum)
                 @error "Stellar spectrum file '$(stellar_spectrum)' does not exist"
+                @error "Try running `\$ ./src/get_data.sh stellar`"
                 return false
             end
 
@@ -1201,7 +1207,7 @@ module atmosphere
         # For now, they are just stored inside the atmos struct
 
         # Print info on the gases
-        @info "Allocated atmosphere with composition:"
+        @info "Allocating atmosphere with composition:"
         gas_flags::String = ""
         g::String = ""
         for i in 1:atmos.gas_num
@@ -1313,6 +1319,7 @@ module atmosphere
             atmos.surface_material = abspath(atmos.surface_material)
             if !isfile(atmos.surface_material)
                 @error "Could not find surface albedo file '$(atmos.surface_material)'"
+                @error "Get these data with `\$ ./src/get_data.sh surfaces`"
                 return false
             end
 

src/energy.jl

@@ -241,13 +241,15 @@ module energy
             # Normalised contribution function (only LW stream contributes)
             fill!(atmos.contfunc_norm,0.0)
             if calc_cf
-                cf_max::Float64 = maximum(atmos.radout.contrib_funcf_band[1,:,:])
+                bw_nm::Float64 = 0.0
                 for ba in 1:atmos.dimen.nd_channel
+                    bw_nm = atmos.bands_wid[ba] * 1e9
                     for lv in 1:atmos.nlev_c
                         atmos.contfunc_norm[lv,ba] =
-                                            atmos.radout.contrib_funcf_band[1,lv,ba]/cf_max
+                                            atmos.radout.contrib_funcf_band[1,lv,ba]/bw_nm
                     end
                 end
+                atmos.contfunc_norm /= maximum(atmos.contfunc_norm)
             end
             atmos.is_out_lw = true
 

src/get_data.sh

@@ -38,10 +38,10 @@ help_surfaces="Get a collection of surface single-scattering albedos"
 help_realgas="Get a real-gas EOS coefficients and lookup tables"
 help_thermo="Get lookup data for thermodynamics (heat capacities, etc.)"
 help="\
-Helper script used to download and unpack data used to run the model.
+Download and unpack data used to run the model.
 
 Call structure:
-    ./get_data [TARGET]
+    $ get_data.sh [TARGET]
 
 Where [TARGET] can be any of the following:
     basic
@@ -57,7 +57,7 @@ Where [TARGET] can be any of the following:
     realgas
         $help_realgas
     thermodynamics
-        $help_thermo
+        $help_thermo\
 "
 
 # Generic OSF downloader function
@@ -194,6 +194,4 @@ function handle_request {
 
 handle_request $1
 
-echo "Done!"
-
 exit 0

src/get_fastchem.sh

@@ -18,5 +18,10 @@ cd build
 cmake ".."
 make
 
-cd ..
-export FC_DIR="$(realpath $fcpath)"
+cd $root
+export FC_DIR=$fcpath
+
+echo "FastChem has been installed"
+echo "It is recommended that you add the following line to your shell rc file"
+echo "export FC_DIR='$fcpath'"
+exit 0

src/get_socrates.sh

@@ -36,7 +36,7 @@ cd "$socpath"
 
 # Environment
 export RAD_DIR=$socpath
-cd ..
+cd $root
 
 # Inform user
 echo "SOCRATES has been installed"

src/phys.jl

@@ -9,8 +9,8 @@ end
 module phys
 
     using NCDatasets
-    using PCHIPInterpolation
     using LoggingExtras
+    import PCHIPInterpolation:Interpolator
 
     # Sources:
     # - Pierrehumbert (2010)

src/plotting.jl

@@ -11,9 +11,9 @@ module plotting
     # Import stuff
     using Plots
     using LaTeXStrings
-    using Glob
     using Printf
     using FFMPEG
+    import Glob:glob
 
     import ..atmosphere
     import ..phys

src/realgas.jl

@@ -12,7 +12,7 @@ module realgas
 
     using ScatteredInterpolation  # 2D interpolation
     using LoggingExtras
-    using DelimitedFiles
+    import DelimitedFiles:readdlm
 
     mutable struct Aqua_t
 

src/setpt.jl

@@ -11,9 +11,9 @@ module setpt
     import ..phys
     import ..atmosphere
 
-    using PCHIPInterpolation
     using NCDatasets
     using LoggingExtras
+    import PCHIPInterpolation:Interpolator
 
     # Read atmosphere T(p) from a CSV file (does not overwrite p_boa and p_toa)
     function fromcsv!(atmos::atmosphere.Atmos_t, fpath::String)

src/spectrum.jl

@@ -12,9 +12,9 @@ module spectrum
 
     using LoggingExtras
     using Printf
-    using PCHIPInterpolation
-    using DelimitedFiles
     using LinearAlgebra
+    import PCHIPInterpolation:Interpolator
+    import DelimitedFiles:readdlm
 
     """
     **Validate spectral file.**